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Fragment of streptococcal M87 protein fused to GCN4 adaptor in complex with human cathelicidin

Analyse Fragment of streptococcal M87 protein fused to GCN4 adaptor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SAY
Type: protein
Length: 315 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General control transcription factor GCN4/M protein chimera; Antibacterial peptide ll-37
UniProt: P03069, Q6TLP8, P49913
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 6 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	General control transcription factor GCN4/M protein chimera	protein	56	91% helix, 0% strand	P03069, Q6TLP8
B	General control transcription factor GCN4/M protein chimera	protein	70	94% helix, 0% strand	P03069, Q6TLP8
E	Antibacterial peptide ll-37	protein	35	74% helix, 0% strand	P49913
C	General control transcription factor GCN4/M protein chimera	protein	53	92% helix, 0% strand	P03069, Q6TLP8
D	General control transcription factor GCN4/M protein chimera	protein	67	97% helix, 0% strand	P03069, Q6TLP8
F	Antibacterial peptide ll-37	protein	34	79% helix, 0% strand	P49913

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, E, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	344	0.56	0.74	24	empty
2	268	0.51	0.73	18	empty
3	137	0.40	0.74	23	EDO

Interfaces

7 interfaces between chains.

A–B · 1332 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1188 Å² buried · 5 hydrogen bonds · protein-protein
C–F · 560 Å² buried · 1 hydrogen bond · protein-protein
A–E · 557 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 304 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7SAY · Fragment of streptococcal M87 protein fused to GCN4 adaptor in complex with human… · the same entry in another collection · chain F against F, TM-score 1.00
P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain C against A, TM-score 0.83
P49913 · AlphaFold monomer V2.0 prediction for cathelicidin antimicrobial peptide (P49913) · a predicted model of the same protein · chain E against A, TM-score 0.62

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03069
Every structure of UniProt Q6TLP8
Every structure of UniProt P49913
Elsewhere: RCSB PDB 7SAY · PDBe 7SAY · UniProt P03069 · UniProt Q6TLP8 · UniProt P49913

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